if the files are part of the loop-back mounted ROM image, you could copy the filesys to your linux PC, mount it, copy all the files recursively to a new directory preserving links, change things around, then make a new filesys with e.g. mkcramfs or mksquashfs (use v2 as v3 of squashfs is incompatible), then copy it to the Z somehow without breaking the currently running image!